header updated

[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 98916e3..a58b6f7 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -42,7 +42,7 @@ public class NJTree
 \r
     //SequenceData is a string representation of what the user\r
     //sees. The display may contain hidden columns.\r
-    CigarArray seqData=null;\r
+    public AlignmentView seqData=null;\r
 \r
     int[] done;\r
     int noseqs;\r
@@ -76,7 +76,7 @@ public class NJTree
      * @param odata Cigar[]\r
      * @param treefile NewickFile\r
      */\r
-    public NJTree(SequenceI[] seqs, CigarArray odata, NewickFile treefile) {\r
+    public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) {\r
       this(seqs, treefile);\r
       if (odata!=null)\r
         seqData = odata;\r
@@ -167,7 +167,7 @@ public class NJTree
      * @param end DOCUMENT ME!\r
      */\r
     public NJTree(SequenceI[] sequence,\r
-                  CigarArray seqData,\r
+                  AlignmentView seqData,\r
                   String type,\r
                   String pwtype,\r
                   int start, int end)\r
@@ -184,8 +184,9 @@ public class NJTree
             {\r
               seqs[i] = new SeqCigar(sequence[i], start, end);\r
             }\r
-            this.seqData = new CigarArray(seqs);\r
-            this.seqData.addOperation(CigarArray.M, end-start+1);\r
+            CigarArray sdata = new CigarArray(seqs);\r
+            sdata.addOperation(CigarArray.M, end-start+1);\r
+            this.seqData = new AlignmentView(sdata);\r
         }\r
 \r
         if (!(type.equals("NJ")))\r
@@ -1018,13 +1019,13 @@ public class NJTree
      *\r
      * @return null or cut'n'pasteable alignment\r
      */\r
-    public String printOriginalSequenceData()\r
+    public String printOriginalSequenceData(char gapChar)\r
     {\r
       if (seqData==null)\r
         return null;\r
-//      return seqData.getSequenceString(Comparison.GapChars[0]);\r
+\r
       StringBuffer sb = new StringBuffer();\r
-      String[] seqdatas = seqData.getSequenceStrings(Comparison.GapChars.charAt(0));\r
+      String[] seqdatas = seqData.getSequenceStrings(gapChar);\r
       for(int i=0; i<seqdatas.length; i++)\r
       {\r
         sb.append(new jalview.util.Format("%-" + 15 + "s").form(\r
@@ -1033,7 +1034,6 @@ public class NJTree
       }\r
       return sb.toString();\r
     }\r
-\r
     /**\r
      * DOCUMENT ME!\r
      *\r